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1. Compound ID: 11621
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a-Psep5Ac7Ac-(2-6)-b-D-Glcp-(1-6)-+
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-3)-b-D-Galp-(1-3)-b-D-GalpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS, polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_147450,IEDB_190606,IEDB_838988,IEDB_838989,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_21,SB_23,SB_24,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 4688
Kenyon JJ, Marzaioli AM, Hall RM, De Castro C "Structure of the K2 capsule associated with the KL2 gene cluster of Acinetobacter baumannii" -
Glycobiology 24(6) (2014) 554-563
The repeat unit structure of the K2 capsule from an extensively antibiotic-resistant Acinetobacter baumannii global clone 2 (GC2) strain was determined. The oligosaccharide contains three simple sugars, d-glucopyranose, d-galatopyranose and N-acetyl-d-galactosamine, and the complex sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (Pse5Ac7Ac or pseudaminic acid), which has not previously been reported in any A. baumannii capsule. The strain was found to carry all the genes required for the synthesis of the sugars and construction of the K2 structure. The linkages catalyzed by the initiating transferase, three glycosyltransferases and the Wzy polymerase were also predicted. Examination of publicly available A. baumannii genome sequences revealed that the same gene cluster, KL2, often occurs in extensively antibiotic-resistant GC2 isolates and in further strain types. The gene module responsible for the synthesis of pseudaminic acid was also detected in four other K loci. A related module including genes for an acylated relative of pseudaminic acid was also found in two new KL types. A polymerase chain reaction scheme was developed to detect all modules containing genes for sugars based on pseudaminic acid and to specifically detect KL2.
Acinetobacter baumannii, capsule polysaccharide, K locus, global clone 2, K2
NCBI PubMed ID: 24688093Publication DOI: 10.1093/glycob/cwu024Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: ruth.hall@sydney.edu.au
Institutions: School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, PCR, GC-MS, sugar analysis, mild acid hydrolysis, chemical methods, genetic methods, bioinformatic analysis
- Article ID: 4721
Senchenkova SN, Shashkov AS, Shneider MM, Arbatsky NP, Popova AV, Miroshnikov KA, Volozhantsev NV, Knirel YA "Structure of the capsular polysaccharide of Acinetobacter baumannii ACICU containing di-N-acetylpseudaminic acid" -
Carbohydrate Research 391 (2014) 89-92
Capsular polysaccharide was isolated by the phenol-water extraction of Acinetobacter baumannii ACICU cells and studied by sugar analysis, partial acid hydrolysis, and 1D and 2D (1)H and (13)C NMR spectroscopy. The polysaccharide was found to contain 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic or di-N-acetylpseudaminic acid (Pse5Ac7Ac), and the following structure of the branched tetrasaccharide repeating unit was established: The genes present in the polysaccharide gene cluster of A. baumannii ACICU are appropriate to the structure established.
Acinetobacter baumannii, pseudaminic acid, capsular polysaccharide structure, polysaccharide gene cluster
NCBI PubMed ID: 24785392Publication DOI: 10.1016/j.carres.2014.04.002Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: Y.A. Knirel
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, GLC, mild acid hydrolysis, chemical methods, NMR-1D, GPC
- Article ID: 4762
Kenyon JJ, Marzaioli AM, Hall RM, De Castro C "Structure of the K6 capsular polysaccharide from Acinetobacter baumannii isolate RBH4" -
Carbohydrate Research 409 (2015) 30-35
The structure of the capsular polysaccharide (CPS) from an Acinetobacter baumannii global clone 2 (GC2) clinical isolate RBH4 that carries the KL6 gene cluster was elucidated by means of chemical and spectroscopical methods. The repeating unit of K6 CPS is linear and contains N-acetyl-D-galactosamine (D-GalpNAc), two D-galactose (D-Galp) residues and 5,7-di-N-acetylpseudaminic acid (Pse5Ac7Ac). The synthesis of these sugars could be attributed to genes in the KL6 capsule biosynthesis gene cluster, and the formation of the linkages between the sugars were assigned to glycosyltransferases or the Wzy polymerase encoded in KL6.
Acinetobacter baumannii, capsular polysaccharide, NMR spectroscopy, pseudaminic acid, K locus, KL6 gene cluster
NCBI PubMed ID: 25917131Publication DOI: 10.1016/j.carres.2015.03.016Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: C. De Castro
Institutions: School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia, Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, Napoli, Italy
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, sugar analysis, enzymatic hydrolysis, extraction, acetylation, bioinformatic analysis, dialysis
- Article ID: 4796
Senchenkova SN, Popova AV, Shashkov AS, Shneider MM, Mei Z, Arbatsky NP, Liu B, Miroshnikov KA, Volozhantsev NV, Knirel YA "Structure of a new pseudaminic acid-containing capsular polysaccharide of Acinetobacter baumannii LUH5550 having the KL42 capsule biosynthesis locus" -
Carbohydrate Research 407 (2015) 154-157
The capsular polysaccharide from Acinetobacter baumannii LUH5550 was studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the branched trisaccharide repeating unit was established: [structure: see text] where Pse5Ac7RHb indicates 5-acetamido-3,5,7,9-tetradeoxy-7-[(R)-3-hydroxybutanoylamino]-L-glycero-L-manno-non-2-ulosonic acid. The genes in the capsule biosynthesis locus designated KL42 are consistent with the structure established.
Acinetobacter baumannii, pseudaminic acid, capsular polysaccharide structure, polysaccharide gene locus
NCBI PubMed ID: 25776191Publication DOI: 10.1016/j.carres.2015.02.006Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: yknirel@gmail.com
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, GPC, bioinformatic analysis
- Article ID: 4819
Giguere D "Surface polysaccharides from Acinetobacter baumannii: Structures and syntheses" -
Carbohydrate Research 418 (2015) 29-43
The emergence of multidrug-resistance Acinetobacter baumannii requires novel approaches for prevention, treatment and diagnosis. The structures of surface polysaccharides from A. baumannii are valuable tools to understand pathogenesis, virulence and immunogenicity. The synthesis of bacterial mono- or polysaccharides may result in novel probes to become important therapeutic options in the fight against A. baumannii. This report exemplifies the relevance of glycochemistry for the development of new antibiotics.
lipopolysaccharides, capsular polysaccharides, Acinetobacter, Acinetobacter baumannii, polysaccharide synthesis, surface polysaccharides
NCBI PubMed ID: 26531136Publication DOI: 10.1016/j.carres.2015.10.001Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: denis.giguere@chm.ulaval.ca
Institutions: Département de Chimie, Université Laval, Québec City, Québec, Canada G1V 0A6
- Article ID: 5458
Kenyon JJ, Arbatsky NP, Shashkov AS, Shneider MM, Popova AV, Hall RM, Knirel YA "Production of the K16 capsular polysaccharide by Acinetobacter baumannii ST25 isolate D4 involves a novel glycosyltransferase encoded in the KL16 gene cluster" -
International Journal of Biological Macromolecules 128 (2019) 101-106
A new capsular polysaccharide (CPS) biosynthesis gene cluster, KL16, was found in the genome sequence of a clinical Acinetobacter baumannii ST25 isolate, D4. The variable part of KL16 contains a module of genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetylpseudaminic acid, Pse5Ac7Ac), a gene encoding ItrA3 that initiates the CPS synthesis with d-GlcpNAc, and two glycosyltransferase (Gtr) genes. The K16 CPS was studied by sugar analysis and Smith degradation along with 1D and 2D 1H and 13C NMR spectroscopy, and shown to be built up of linear trisaccharide repeats containing d-galactose (d-Gal), N-acetyl-d-glucosamine (d-GlcNAc), and Pse5Ac7Ac. The d-Galp residue is linked to the d-GlcpNAc initiating sugar via a β-(1→3) linkage evidently formed by a Gtr5 variant, Gtr5K16, encoded in KL16. This reveals an altered or relaxed substrate specificity of this variant as the majority of Gtr5-type glycosyltransferases have previously been shown to form a β-d-Galp-(1→3)-d-GalpNAc linkage. The β-Psep5Ac7Ac-(2→4)-d-Galp linkage is predicted to be formed by the other glycosyltransferase, Gtr37, which does not match members of any known glycosyltransferase family.
Acinetobacter baumannii, capsular polysaccharide, 5, glycosyltransferase, 7-Di-N-acetylpseudaminic acid, KL16 K locus
NCBI PubMed ID: 30664967Publication DOI: 10.1016/j.ijbiomac.2019.01.080Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: J.J. Kenyon
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, Smith degradation, function analysis of gene clusters
- Article ID: 5500
Singh JK, Adams FG, Brown MH "Diversity and Function of Capsular Polysaccharide in Acinetobacter baumannii" -
Frontiers in Microbiology 9 (2019) 3301
The Gram-negative opportunistic bacterium Acinetobacter baumannii is a significant cause of hospital-borne infections worldwide. Alarmingly, the rapid development of antimicrobial resistance coupled with the remarkable ability of isolates to persist on surfaces for extended periods of time has led to infiltration of A. baumannii into our healthcare environments. A major virulence determinant of A. baumannii is the presence of a capsule that surrounds the bacterial surface. This capsule is comprised of tightly packed repeating polysaccharide units which forms a barrier around the bacterial cell wall, providing protection from environmental pressures including desiccation and disinfection regimes as well as host immune responses such as serum complement. Additionally, capsule has been shown to confer resistance to a range of clinically relevant antimicrobial compounds. Distressingly, treatment options for A. baumannii infections are becoming increasingly limited, and the urgency to develop effective infection control strategies and therapies to combat infections is apparent. An increased understanding of the contribution of capsule to the pathobiology of A. baumannii is required to determine its feasibility as a target for new strategies to combat drug resistant infections. Significant variation in capsular polysaccharide structures between A. baumannii isolates has been identified, with over 100 distinct capsule types, incorporating a vast variety of sugars. This review examines the studies undertaken to elucidate capsule diversity and advance our understanding of the role of capsule in A. baumannii pathogenesis.
polysaccharide, Acinetobacter, Acinetobacter baumannii, capsule, virulence factor, persistence
NCBI PubMed ID: 30687280Publication DOI: 10.3389/fmicb.2018.03301Journal NLM ID: 101548977Publisher: Lausanne: Frontiers Research Foundation
Correspondence: Melissa H. Brown
Institutions: College of Science and Engineering, Flinders University, Bedford Park, SA, Australia.College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
- Article ID: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
- Article ID: 6413
Knirel YA, Kasimova AA, Arbatsky NP, Shneider MM, Popova AV, Brovko FA, Shashkov AS, Senchenkova SN, Perepelov AV, Shpirt AM "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic Acids in the Capsular Polysaccharides of Acinetobacter baumannii" -
Biochemistry (Moscow) 88(2) (2023) 202-210
The polysaccharide capsule surrounding bacterial cell plays an important role in pathogenesis of infections caused by the opportunistic pathogen Acinetobacter baumannii by providing protection from external factors. The structures of the capsular polysaccharide (CPS) produced by A. baumannii isolates and the corresponding CPS biosynthesis gene clusters are highly diverse, although many of them are related. Many types of A. baumannii CPSs contain isomers of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acid (DTNA). Three of these isomers, namely acinetaminic acid (l-glycero-l-altro isomer), 8-epiacinetaminic acid (d-glycero-l-altro isomer), and 8-epipseudaminic acid (d-glycero-l-manno isomer), have not been found so far in naturally occurring carbohydrates from other species. In A. baumannii CPSs, DTNAs carry N-acyl substituents at positions 5 and 7; in some CPSs, both N-acetyl and N-(3-hydroxybutanoyl) groups are present. Remarkably, pseudaminic acid carries the (R)-isomer and legionaminic acid carries the (S)-isomer of the 3-hydroxybutanoyl group. The review addresses the structure and genetics of biosynthesis of A. baumannii CPSs containing di-N-acyl derivatives of DTNA.
Acinetobacter baumannii, capsular polysaccharide, nonulosonic acid, Bacterial polysaccharide, capsule, higher monosaccharide, acyl group
NCBI PubMed ID: 37072328Publication DOI: 10.1134/S0006297923020049Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: Y.A. Knirel
Institutions: State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia, Branch of the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry in Pushchino, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
- Article ID: 6520
Wang H, Zeng P, Zhang P, Zuo Z, Liu Y, Xia J, Lam JKW, Chan HK, Leung SSY "Phage-derived polysaccharide depolymerase potentiates ceftazidime efficacy against Acinetobacter baumannii pneumonia via low-serum-dependent mechanisms" -
International Journal of Biological Macromolecules 282(Pt6) (2024) ID 137486
The emergence of multidrug-resistant Acinetobacter baumannii (MDR-AB), which most commonly manifests as pneumonia, has posed significant clinical challenges and called for novel treatment strategies. Phage depolymerases, which degrade bacterial surface carbohydrates, have emerged as potential antimicrobial agents. However, their preclinical application is limited to systemic infections due to their dependency on serum-mediated bacterial killing. To extend the treatment paradigm of depolymerase to low-serum lung infections, we explored the feasibility of applying phage depolymerase to potentiate antibiotic efficacy in controlling MDR-AB pneumonia. Using a model depolymerase, Dpo71, we observed that it could effectively potentiate antibiotic efficacy against MDR-AB2 bacteria in low-serum conditions mimicking lung milieu but showed no adjuvant effect in serum-free conditions. Unprecedentedly, we reported this low-serum-dependent mechanism that polysaccharide-degrading enzyme Dpo71 exposed bacteria to serum-induced membrane permeabilization and oxidative phosphorylation pathway inhibition, leading to a weakened ATP-dependent efflux pump and strengthened ROS-induced membrane permeabilization. These joint effects facilitated antibiotic (ceftazidime, CFZ) binding, ultimately exerting bactericidal effects. Resultantly, the bacterial load in the lungs of the Dpo71-CFZ combination group was significantly reduced compared with the Dpo71-alone and CFZ-alone groups. Overall, this study unravels the low-serum-dependent mechanisms by which depolymerase potentiated antibiotic efficacy, highlighting its potential as a novel strategy to enhance antibiotic activity against severe pneumonia
serum, Acinetobacter baumannii pneumonia, antibiotic potentiation, multidrug-resistance, phage-derived polysaccharide depolymerases, synergism
NCBI PubMed ID: 39528188Publication DOI: 10.1016/j.ijbiomac.2024.137486Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: sharon.leung@cuhk.edu.hk
Institutions: School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China, Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China, Department of Chemistry, the Chinese University of Hong Kong, Hong Kong, China, Department of Pharmaceutics, UCL School of Pharmacy, University College London, London, UK, Sydney Pharmacy School, University of Sydney, Sydney, Australia
Methods: DNA sequencing, biological assays, extraction, dialysis, spectrophotometry, TEM, centrifugation, gene cloning, column chromatography, gene techniques, MIC assay, inhibition assay, binding assay
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2. Compound ID: 15844
Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_142488,IEDB_143260,IEDB_146664,IEDB_147450,IEDB_190606,IEDB_838988,IEDB_885822,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_23,SB_24,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
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3. Compound ID: 15845
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a-Psep5Ac7Ac-(2-6)-b-D-Glcp-(1-6)-+
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a-Psep5Ac7Ac-(2-6)-b-D-Glcp-(1-6)-b-D-Galp-(1-3)-b-D-GalpNAc-(1-3)-b-D-Galp-(1-3)-D-GalpNAc |
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Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_142488,IEDB_143260,IEDB_146664,IEDB_147450,IEDB_190606,IEDB_838988,IEDB_838989,IEDB_885822,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_21,SB_23,SB_24,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
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